def test_fwdti_predictions():
# single voxel case
gtf = 0.50 # ground truth volume fraction
angles = [(90, 0), (90, 0)]
mevals = np.array([[0.0017, 0.0003, 0.0003], [0.003, 0.003, 0.003]])
S_conta, peaks = multi_tensor(gtab_2s, mevals, S0=100,
angles=angles,
fractions=[(1-gtf) * 100, gtf*100], snr=None)
R = all_tensor_evecs(peaks[0])
R = R.reshape((9))
model_params = np.concatenate(([0.0017, 0.0003, 0.0003], R, [gtf]),
axis=0)
S_pred1 = fwdti_prediction(model_params, gtab_2s, S0=100)
assert_array_almost_equal(S_pred1, S_conta)
# Testing in model class
fwdm = fwdti.FreeWaterTensorModel(gtab_2s)
S_pred2 = fwdm.predict(model_params, S0=100)
assert_array_almost_equal(S_pred2, S_conta)
# Testing in fit class
fwefit = fwdm.fit(S_conta)
S_pred3 = fwefit.predict(gtab_2s, S0=100)
assert_array_almost_equal(S_pred3, S_conta, decimal=5)
# Multi voxel simulation
S_pred1 = fwdti_prediction(model_params_mv, gtab_2s, S0=100) # function
assert_array_almost_equal(S_pred1, DWI)
S_pred2 = fwdm.predict(model_params_mv, S0=100) # Model class
assert_array_almost_equal(S_pred2, DWI)
fwefit = fwdm.fit(DWI) # Fit class
S_pred3 = fwefit.predict(gtab_2s, S0=100)
assert_array_almost_equal(S_pred3, DWI)
def test_sphere_scaling_csdmodel():
"""Check that mirroring regularization sphere does not change the result of
the model"""
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = multi_tensor(gtab, mevals, 100., angles=angles,
fractions=[50, 50], snr=None)
hemi = small_sphere
sphere = hemi.mirror()
response = (np.array([0.0015, 0.0003, 0.0003]), 100)
model_full = ConstrainedSphericalDeconvModel(gtab, response,
reg_sphere=sphere)
model_hemi = ConstrainedSphericalDeconvModel(gtab, response,
reg_sphere=hemi)
csd_fit_full = model_full.fit(S)
csd_fit_hemi = model_hemi.fit(S)
assert_array_almost_equal(csd_fit_full.shm_coeff, csd_fit_hemi.shm_coeff)
def test_peaksFromModelParallel():
SNR = 100
S0 = 100
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
data, _ = multi_tensor(gtab, mevals, S0, angles=[(0, 0), (60, 0)],
fractions=[50, 50], snr=SNR)
# test equality with/without multiprocessing
model = SimpleOdfModel()
pam_multi = peaks_from_model(model, data, _sphere, .5, 45,
normalize_peaks=True, return_odf=True,
return_sh=True, parallel=True)
pam_single = peaks_from_model(model, data, _sphere, .5, 45,
normalize_peaks=True, return_odf=True,
return_sh=True, parallel=False)
assert_array_almost_equal(pam_multi.gfa, pam_single.gfa)
assert_array_almost_equal(pam_multi.qa, pam_single.qa)
assert_array_almost_equal(pam_multi.peak_values, pam_single.peak_values)
assert_array_equal(pam_multi.peak_indices, pam_single.peak_indices)
assert_array_almost_equal(pam_multi.peak_dirs, pam_single.peak_dirs)
assert_array_almost_equal(pam_multi.shm_coeff, pam_single.shm_coeff)
assert_array_almost_equal(pam_multi.odf, pam_single.odf)
def test_minmax_normalize():
bvalue = 3000
S0 = 1
SNR = 100
sphere = get_sphere("symmetric362")
bvecs = np.concatenate(([[0, 0, 0]], sphere.vertices))
bvals = np.zeros(len(bvecs)) + bvalue
bvals[0] = 0
gtab = gradient_table(bvals, bvecs)
evals = np.array(([0.0017, 0.0003, 0.0003], [0.0017, 0.0003, 0.0003]))
S, sticks = multi_tensor(gtab, evals, S0, angles=[(0, 0), (90, 0)], fractions=[50, 50], snr=SNR)
odf = multi_tensor_odf(sphere.vertices, evals, angles=[(0, 0), (90, 0)], fractions=[50, 50])
odf2 = minmax_normalize(odf)
assert_equal(odf2.max(), 1)
assert_equal(odf2.min(), 0)
odf3 = np.empty(odf.shape)
odf3 = minmax_normalize(odf, odf3)
assert_equal(odf3.max(), 1)
assert_equal(odf3.min(), 0)
def test_r2_term_odf_sharp():
SNR = None
S0 = 1
angle = 75
_, fbvals, fbvecs = get_data('small_64D') #get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
sphere = get_sphere('symmetric724')
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
S, sticks = multi_tensor(gtab, mevals, S0, angles=[(0, 0), (angle, 0)],
fractions=[50, 50], snr=SNR)
mevecs = [all_tensor_evecs(sticks[0]).T,
all_tensor_evecs(sticks[1]).T]
odf_gt = multi_tensor_odf(sphere.vertices, [0.5, 0.5], mevals, mevecs)
odfs_sh = sf_to_sh(odf_gt, sphere, sh_order=8, basis_type=None)
fodf_sh = odf_sh_to_sharp(odfs_sh, sphere, basis=None, ratio=3 / 15.,
sh_order=8, lambda_=1., tau=0.1, r2_term=True)
fodf = sh_to_sf(fodf_sh, sphere, sh_order=8, basis_type=None)
directions_gt, _, _ = peak_directions(odf_gt, sphere)
directions, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions_gt, directions)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
def _compute_voxel(args):
"""
Simulate DW signal for one voxel. Uses the multi-tensor model and
three isotropic compartments.
Apparent diffusivity tensors are taken from [Alexander2002]_
and [Pierpaoli1996]_.
.. [Alexander2002] Alexander et al., Detection and modeling of non-Gaussian
apparent diffusion coefficient profiles in human brain data, MRM
48(2):331-340, 2002, doi: `10.1002/mrm.10209
<http://dx.doi.org/10.1002/mrm.10209>`_.
.. [Pierpaoli1996] Pierpaoli et al., Diffusion tensor MR imaging
of the human brain, Radiology 201:637-648. 1996.
"""
ffs = args["fractions"]
gtab = args["gradients"]
signal = np.zeros_like(gtab.bvals, dtype=np.float32)
# Simulate dwi signal
sf_vf = np.sum(ffs)
if sf_vf > 0.0:
ffs = (np.array(ffs) / sf_vf) * 100
snr = args["snr"] if args["snr"] > 0 else None
try:
signal, _ = multi_tensor(gtab, args["mevals"], S0=args["S0"], angles=args["sticks"], fractions=ffs, snr=snr)
except Exception as e:
pass
# iflogger.warn('Exception simulating dwi signal: %s' % e)
return signal.tolist()
def test_csd_predict():
"""
"""
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
response = (np.array([0.0015, 0.0003, 0.0003]), S0)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(S)
prediction = csd_predict(csd_fit.shm_coeff, gtab, response=response, S0=S0)
npt.assert_equal(prediction.shape[0], S.shape[0])
model_prediction = csd.predict(csd_fit.shm_coeff)
assert_array_almost_equal(prediction, model_prediction)
# Roundtrip tests (quite inaccurate, because of regularization):
assert_array_almost_equal(csd_fit.predict(gtab, S0=S0),S,decimal=1)
assert_array_almost_equal(csd.predict(csd_fit.shm_coeff, S0=S0),S,decimal=1)
def test_exponential_iso():
fdata, fbvals, fbvecs = dpd.get_data()
data_dti = nib.load(fdata).get_data()
gtab_dti = grad.gradient_table(fbvals, fbvecs)
data_multi, gtab_multi = dpd.dsi_deconv_voxels()
for data, gtab in zip([data_dti, data_multi], [gtab_dti, gtab_multi]):
sfmodel = sfm.SparseFascicleModel(
gtab, isotropic=sfm.ExponentialIsotropicModel)
sffit1 = sfmodel.fit(data[0, 0, 0])
sphere = dpd.get_sphere()
odf1 = sffit1.odf(sphere)
pred1 = sffit1.predict(gtab)
SNR = 1000
S0 = 100
mevals = np.array(([0.0015, 0.0005, 0.0005],
[0.0015, 0.0005, 0.0005]))
angles = [(0, 0), (60, 0)]
S, sticks = sims.multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
sffit = sfmodel.fit(S)
pred = sffit.predict()
npt.assert_(xval.coeff_of_determination(pred, S) > 96)
def test_dki_micro_predict_single_voxel():
# single fiber simulate (which is the assumption of our model)
fie = 0.49
ADi = 0.00099
ADe = 0.00226
RDi = 0
RDe = 0.00087
# prepare simulation:
theta = random.uniform(0, 180)
phi = random.uniform(0, 320)
angles = [(theta, phi), (theta, phi)]
mevals = np.array([[ADi, RDi, RDi], [ADe, RDe, RDe]])
frac = [fie*100, (1 - fie)*100]
signal, dt, kt = multi_tensor_dki(gtab_2s, mevals, angles=angles,
fractions=frac, snr=None)
signal_gt, da = multi_tensor(gtab_2s, mevals, angles=angles,
fractions=frac, snr=None)
# Defined DKI microstrutural model
dkiM = dki_micro.KurtosisMicrostructureModel(gtab_2s)
# Fit single voxel signal
dkiF = dkiM.fit(signal)
# Check predict of KurtosisMicrostruturalModel
pred = dkiM.predict(dkiF.model_params)
assert_array_almost_equal(pred, signal_gt, decimal=4)
pred = dkiM.predict(dkiF.model_params, S0=100)
assert_array_almost_equal(pred, signal_gt * 100, decimal=4)
# Check predict of KurtosisMicrostruturalFit
pred = dkiF.predict(gtab_2s, S0=100)
assert_array_almost_equal(pred, signal_gt * 100, decimal=4)
def test_csd_superres():
""" Check the quality of csdfit with high SH order. """
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
# img, gtab = read_stanford_hardi()
evals = np.array([[1.5, .3, .3]]) * [[1.], [1.]] / 1000.
S, sticks = multi_tensor(gtab, evals, snr=None, fractions=[55., 45.])
model16 = ConstrainedSphericalDeconvModel(gtab, (evals[0], 3.),
sh_order=16)
fit16 = model16.fit(S)
# print local_maxima(fit16.odf(default_sphere), default_sphere.edges)
d, v, ind = peak_directions(fit16.odf(default_sphere), default_sphere,
relative_peak_threshold=.2,
min_separation_angle=0)
# Check that there are two peaks
assert_equal(len(d), 2)
# Check that peaks line up with sticks
cos_sim = abs((d * sticks).sum(1)) ** .5
assert_(all(cos_sim > .99))
def test_bdg_initial_direction():
"""This test the number of inital direction."
"""
hsph_updated = HemiSphere.from_sphere(unit_icosahedron).subdivide(2)
vertices = hsph_updated.vertices
bvecs = vertices
bvals = np.ones(len(vertices)) * 1000
bvecs = np.insert(bvecs, 0, np.array([0, 0, 0]), axis=0)
bvals = np.insert(bvals, 0, 0)
gtab = gradient_table(bvals, bvecs)
# test that we get one direction when we have a single tensor
voxel = single_tensor(gtab).reshape([1, 1, 1, -1])
dti_model = dti.TensorModel(gtab)
boot_dg = BootDirectionGetter.from_data(voxel, dti_model, 30, sh_order=6)
initial_direction = boot_dg.initial_direction(np.zeros(3))
npt.assert_equal(len(initial_direction), 1)
npt.assert_allclose(initial_direction[0], [1, 0, 0], atol=0.1)
# test that we get multiple directions when we have a multi-tensor
mevals = np.array([[1.5, 0.4, 0.4], [1.5, 0.4, 0.4]]) * 1e-3
fracs = [60, 40]
voxel, primary_evecs = multi_tensor(gtab, mevals, fractions=fracs,
snr=None)
voxel = voxel.reshape([1, 1, 1, -1])
response = (np.array([0.0015, 0.0004, 0.0004]), 1)
csd_model = ConstrainedSphericalDeconvModel(gtab, response=response,
sh_order=4)
boot_dg = BootDirectionGetter.from_data(voxel, csd_model, 30)
initial_direction = boot_dg.initial_direction(np.zeros(3))
npt.assert_equal(len(initial_direction), 2)
npt.assert_allclose(initial_direction, primary_evecs, atol=0.1)
def test_odfdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
e1 = 15.0
e2 = 3.0
ratio = e2 / e1
csd = ConstrainedSDTModel(gtab, ratio, None)
csd_fit = csd.fit(S)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=10)
assert_equal(len(w) > 0, True)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=8)
assert_equal(len(w) > 0, False)
csd_fit = csd.fit(np.zeros_like(S))
fodf = csd_fit.odf(sphere)
assert_array_equal(fodf, np.zeros_like(fodf))
odf_sh = np.zeros_like(fodf)
odf_sh[1] = np.nan
fodf, it = odf_deconv(odf_sh, csd.R, csd.B_reg)
assert_array_equal(fodf, np.zeros_like(fodf))
def simulated_data(gtab, S0=100, SNR=100):
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
S, sticks = multi_tensor(gtab, mevals, S0, angles=[(0, 0), (90, 0)], fractions=[50, 50], snr=SNR)
ratio = 3 / 15.0
return S, ratio
def test_reconst_ivim():
with TemporaryDirectory() as out_dir:
bvals = np.array([0., 10., 20., 30., 40., 60., 80., 100.,
120., 140., 160., 180., 200., 300., 400.,
500., 600., 700., 800., 900., 1000.])
N = len(bvals)
bvecs = generate_bvecs(N)
temp_bval_path = pjoin(out_dir, "temp.bval")
np.savetxt(temp_bval_path, bvals)
temp_bvec_path = pjoin(out_dir, "temp.bvec")
np.savetxt(temp_bvec_path, bvecs)
gtab = gradient_table(bvals, bvecs)
S0, f, D_star, D = 1000.0, 0.132, 0.00885, 0.000921
mevals = np.array(([D_star, D_star, D_star], [D, D, D]))
# This gives an isotropic signal.
data = multi_tensor(gtab, mevals, snr=None, S0=S0,
fractions=[f * 100, 100 * (1 - f)])
# Single voxel data
data_single = data[0]
temp_affine = np.eye(4)
data_multi = np.zeros((2, 2, 1, len(gtab.bvals)))
data_multi[0, 0, 0] = data_multi[0, 1, 0] = data_multi[
1, 0, 0] = data_multi[1, 1, 0] = data_single
data_img = nib.Nifti1Image(data_multi.astype(int), temp_affine)
data_path = pjoin(out_dir, 'tmp_data.nii.gz')
nib.save(data_img, data_path)
mask = np.ones_like(data_multi[..., 0])
mask_img = nib.Nifti1Image(mask.astype(np.uint8), data_img.affine)
mask_path = pjoin(out_dir, 'tmp_mask.nii.gz')
nib.save(mask_img, mask_path)
ivim_flow = ReconstIvimFlow()
args = [data_path, temp_bval_path, temp_bvec_path, mask_path]
ivim_flow.run(*args, out_dir=out_dir)
S0_path = ivim_flow.last_generated_outputs['out_S0_predicted']
S0_data = nib.load(S0_path).get_data()
assert_equal(S0_data.shape, data_img.shape[:-1])
f_path = ivim_flow.last_generated_outputs['out_perfusion_fraction']
f_data = nib.load(f_path).get_data()
assert_equal(f_data.shape, data_img.shape[:-1])
D_star_path = ivim_flow.last_generated_outputs['out_D_star']
D_star_data = nib.load(D_star_path).get_data()
assert_equal(D_star_data.shape, data_img.shape[:-1])
D_path = ivim_flow.last_generated_outputs['out_D']
D_data = nib.load(D_path).get_data()
assert_equal(D_data.shape, data_img.shape[:-1])
def test_multiple_b0():
# Generate a signal with multiple b0
# This gives an isotropic signal.
signal = multi_tensor(gtab_with_multiple_b0, mevals, snr=None, S0=S0,
fractions=[f * 100, 100 * (1 - f)])
# Single voxel data
data_single = signal[0]
ivim_model_multiple_b0 = IvimModel(gtab_with_multiple_b0)
x0_estimated = ivim_model_multiple_b0.fit(data_single)
def test_csdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
S, sticks = multi_tensor(gtab, mevals, S0, angles=[(0, 0), (60, 0)],
fractions=[50, 50], snr=SNR)
sphere = get_sphere('symmetric724')
mevecs = [all_tensor_evecs(sticks[0]).T,
all_tensor_evecs(sticks[1]).T]
odf_gt = multi_tensor_odf(sphere.vertices, [0.5, 0.5], mevals, mevecs)
response = (np.array([0.0015, 0.0003, 0.0003]), S0)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(S)
assert_equal(csd_fit.shm_coeff[0] > 0, True)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
ConstrainedSphericalDeconvModel(gtab, response, sh_order=10)
assert_equal(len(w) > 0, True)
with warnings.catch_warnings(record=True) as w:
ConstrainedSphericalDeconvModel(gtab, response, sh_order=8)
assert_equal(len(w) > 0, False)
def setup_module():
"""Module-level setup"""
global gtab, gtab_2s, mevals, model_params_mv
global DWI, FAref, GTF, MDref, FAdti, MDdti
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs)
# FW model requires multishell data
bvals_2s = np.concatenate((bvals, bvals * 1.5), axis=0)
bvecs_2s = np.concatenate((bvecs, bvecs), axis=0)
gtab_2s = gradient_table(bvals_2s, bvecs_2s)
# Simulation a typical DT and DW signal for no water contamination
S0 = np.array(100)
dt = np.array([0.0017, 0, 0.0003, 0, 0, 0.0003])
evals, evecs = decompose_tensor(from_lower_triangular(dt))
S_tissue = single_tensor(gtab_2s, S0=100, evals=evals, evecs=evecs,
snr=None)
dm = dti.TensorModel(gtab_2s, 'WLS')
dtifit = dm.fit(S_tissue)
FAdti = dtifit.fa
MDdti = dtifit.md
dtiparams = dtifit.model_params
# Simulation of 8 voxels tested
DWI = np.zeros((2, 2, 2, len(gtab_2s.bvals)))
FAref = np.zeros((2, 2, 2))
MDref = np.zeros((2, 2, 2))
# Diffusion of tissue and water compartments are constant for all voxel
mevals = np.array([[0.0017, 0.0003, 0.0003], [0.003, 0.003, 0.003]])
# volume fractions
GTF = np.array([[[0.06, 0.71], [0.33, 0.91]],
[[0., 0.], [0., 0.]]])
# S0 multivoxel
S0m = 100 * np.ones((2, 2, 2))
# model_params ground truth (to be fill)
model_params_mv = np.zeros((2, 2, 2, 13))
for i in range(2):
for j in range(2):
gtf = GTF[0, i, j]
S, p = multi_tensor(gtab_2s, mevals, S0=100,
angles=[(90, 0), (90, 0)],
fractions=[(1-gtf) * 100, gtf*100], snr=None)
DWI[0, i, j] = S
FAref[0, i, j] = FAdti
MDref[0, i, j] = MDdti
R = all_tensor_evecs(p[0])
R = R.reshape((9))
model_params_mv[0, i, j] = \
np.concatenate(([0.0017, 0.0003, 0.0003], R, [gtf]), axis=0)
def test_csd_predict():
"""
Test prediction API
"""
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
sphere = small_sphere
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
response = (np.array([0.0015, 0.0003, 0.0003]), S0)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(S)
# Predicting from a fit should give the same result as predicting from a
# model, S0 is 1 by default
prediction1 = csd_fit.predict()
prediction2 = csd.predict(csd_fit.shm_coeff)
npt.assert_array_equal(prediction1, prediction2)
npt.assert_array_equal(prediction1[..., gtab.b0s_mask], 1.)
# Same with a different S0
prediction1 = csd_fit.predict(S0=123.)
prediction2 = csd.predict(csd_fit.shm_coeff, S0=123.)
npt.assert_array_equal(prediction1, prediction2)
npt.assert_array_equal(prediction1[..., gtab.b0s_mask], 123.)
# For "well behaved" coefficients, the model should be able to find the
# coefficients from the predicted signal.
coeff = np.random.random(csd_fit.shm_coeff.shape) - .5
coeff[..., 0] = 10.
S = csd.predict(coeff)
csd_fit = csd.fit(S)
npt.assert_array_almost_equal(coeff, csd_fit.shm_coeff)
# Test predict on nd-data set
S_nd = np.zeros((2, 3, 4, S.size))
S_nd[:] = S
fit = csd.fit(S_nd)
predict1 = fit.predict()
predict2 = csd.predict(fit.shm_coeff)
npt.assert_array_almost_equal(predict1, predict2)
def sim_tensor_2x(gtab, angle=90, sphere=None, S0=1., snr=None):
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
data, sticks = multi_tensor(gtab, mevals, S0,
angles=[(90 , 0), (90, angle)],
fractions=[50, 50], snr=snr)
mevecs = [all_tensor_evecs(sticks[0]).T,
all_tensor_evecs(sticks[1]).T]
odf_gt = multi_tensor_odf(sphere.vertices, [0.5, 0.5], mevals, mevecs)
return data, sticks, odf_gt
def test_predict():
SNR = 1000
S0 = 1
_, fbvals, fbvecs = dpd.get_data("small_64D")
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = grad.gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = sims.multi_tensor(gtab, mevals, S0, angles=angles, fractions=[50, 50], snr=SNR)
sfmodel = sfm.SparseFascicleModel(gtab, response=[0.0015, 0.0003, 0.0003])
sffit = sfmodel.fit(S)
pred = sffit.predict()
npt.assert_almost_equal(pred, S, decimal=1)
def test_fwdti_precision():
# Simulation when water contamination is added
gtf = 0.63416 # ground truth volume fraction
mevals = np.array([[0.0017, 0.0003, 0.0003], [0.003, 0.003, 0.003]])
S_conta, peaks = multi_tensor(gtab_2s, mevals, S0=100,
angles=[(90, 0), (90, 0)],
fractions=[(1-gtf) * 100, gtf*100], snr=None)
fwdm = fwdti.FreeWaterTensorModel(gtab_2s, 'WLS', piterations=5)
fwefit = fwdm.fit(S_conta)
FAfwe = fwefit.fa
Ffwe = fwefit.f
MDfwe = fwefit.md
assert_almost_equal(FAdti, FAfwe, decimal=5)
assert_almost_equal(Ffwe, gtf, decimal=5)
assert_almost_equal(MDfwe, MDdti, decimal=5)
def test_fwdti_restore():
# Restore has to work well even in nonproblematic cases
# Simulate a signal corrupted by free water diffusion contamination
gtf = 0.50 # ground truth volume fraction
mevals = np.array([[0.0017, 0.0003, 0.0003], [0.003, 0.003, 0.003]])
S_conta, peaks = multi_tensor(gtab_2s, mevals, S0=100,
angles=[(90, 0), (90, 0)],
fractions=[(1-gtf) * 100, gtf*100], snr=None)
fwdm = fwdti.FreeWaterTensorModel(gtab_2s, 'NLS', weighting='sigma',
sigma=4)
fwdtiF = fwdm.fit(S_conta)
assert_array_almost_equal(fwdtiF.fa, FAdti)
assert_array_almost_equal(fwdtiF.f, gtf)
fwdm2 = fwdti.FreeWaterTensorModel(gtab_2s, 'NLS', weighting='gmm')
fwdtiF2 = fwdm2.fit(S_conta)
assert_array_almost_equal(fwdtiF2.fa, FAdti)
assert_array_almost_equal(fwdtiF2.f, gtf)
def test_peaks_shm_coeff():
SNR = 100
S0 = 100
_, fbvals, fbvecs = get_data('small_64D')
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
data, _ = multi_tensor(gtab, mevals, S0, angles=[(0, 0), (60, 0)],
fractions=[50, 50], snr=SNR)
from dipy.reconst.shm import CsaOdfModel
model = CsaOdfModel(gtab, 4)
pam = peaks_from_model(model, data[None,:], sphere, .5, 45,
return_odf=True, return_sh=True)
# Test that spherical harmonic coefficients return back correctly
B = np.linalg.pinv(pam.invB)
odf2 = np.dot(pam.shm_coeff, B)
assert_array_almost_equal(pam.odf, odf2)
assert_equal(pam.shm_coeff.shape[-1], 45)
pam = peaks_from_model(model, data[None,:], sphere, .5, 45,
return_odf=True, return_sh=False)
assert_equal(pam.shm_coeff, None)
pam = peaks_from_model(model, data[None, :], sphere, .5, 45,
return_odf=True, return_sh=True,
sh_basis_type='mrtrix')
B = np.linalg.pinv(pam.invB)
odf2 = np.dot(pam.shm_coeff, B)
assert_array_almost_equal(pam.odf, odf2)
def test_r2_term_odf_sharp():
SNR = None
S0 = 1
angle = 45 #45 degrees is a very tight angle to disentangle
_, fbvals, fbvecs = get_data('small_64D') #get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
sphere = get_sphere('symmetric724')
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (angle, 0)]
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
odfs_sh = sf_to_sh(odf_gt, sphere, sh_order=8, basis_type=None)
fodf_sh = odf_sh_to_sharp(odfs_sh, sphere, basis=None, ratio=3 / 15.,
sh_order=8, lambda_=1., tau=0.1, r2_term=True)
fodf = sh_to_sf(fodf_sh, sphere, sh_order=8, basis_type=None)
directions_gt, _, _ = peak_directions(odf_gt, sphere)
directions, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions_gt, directions)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
# This should pass as well
sdt_model = ConstrainedSDTModel(gtab, ratio=3/15., sh_order=8)
sdt_fit = sdt_model.fit(S)
fodf = sdt_fit.odf(sphere)
directions_gt, _, _ = peak_directions(odf_gt, sphere)
directions, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions_gt, directions)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
def test_with_higher_S0():
"""
Test whether fitting works for S0 > 1.
"""
# params for a single voxel
S0_2 = 1000.
params2 = np.array([S0_2, f, D_star, D])
mevals2 = np.array(([D_star, D_star, D_star], [D, D, D]))
# This gives an isotropic signal.
signal2 = multi_tensor(gtab, mevals2, snr=None, S0=S0_2,
fractions=[f * 100, 100 * (1 - f)])
# Single voxel data
data_single2 = signal2[0]
ivim_fit = ivim_model.fit(data_single2)
est_signal = ivim_fit.predict(gtab)
assert_array_equal(est_signal.shape, data_single2.shape)
assert_array_almost_equal(est_signal, data_single2)
assert_array_almost_equal(ivim_fit.model_params, params2)
def test_sfm_stick():
fdata, fbvals, fbvecs = dpd.get_data()
data = nib.load(fdata).get_data()
gtab = grad.gradient_table(fbvals, fbvecs)
sfmodel = sfm.SparseFascicleModel(gtab, solver="NNLS", response=[0.001, 0, 0])
sffit1 = sfmodel.fit(data[0, 0, 0])
sphere = dpd.get_sphere("symmetric642")
odf1 = sffit1.odf(sphere)
pred1 = sffit1.predict(gtab)
SNR = 1000
S0 = 1
mevals = np.array(([0.001, 0, 0], [0.001, 0, 0]))
angles = [(0, 0), (60, 0)]
S, sticks = sims.multi_tensor(gtab, mevals, S0, angles=angles, fractions=[50, 50], snr=SNR)
sfmodel = sfm.SparseFascicleModel(gtab, solver="NNLS", response=[0.001, 0, 0])
sffit = sfmodel.fit(S)
pred = sffit.predict()
npt.assert_almost_equal(pred, S, decimal=1)
def test_odf_sh_to_sharp():
SNR = None
S0 = 1
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
S, sticks = multi_tensor(gtab, mevals, S0, angles=[(10, 0), (100, 0)],
fractions=[50, 50], snr=SNR)
sphere = get_sphere('symmetric724')
qb = QballModel(gtab, sh_order=8, assume_normed=True)
qbfit = qb.fit(S)
odf_gt = qbfit.odf(sphere)
Z = np.linalg.norm(odf_gt)
odfs_gt = np.zeros((3, 1, 1, odf_gt.shape[0]))
odfs_gt[:,:,:] = odf_gt[:]
odfs_sh = sf_to_sh(odfs_gt, sphere, sh_order=8, basis_type=None)
odfs_sh /= Z
fodf_sh = odf_sh_to_sharp(odfs_sh, sphere, basis=None, ratio=3 / 15.,
sh_order=8, lambda_=1., tau=0.1)
fodf = sh_to_sf(fodf_sh, sphere, sh_order=8, basis_type=None)
directions2, _, _ = peak_directions(fodf[0, 0, 0], sphere)
assert_equal(directions2.shape[0], 2)
def test_predict():
SNR = 1000
S0 = 100
_, fbvals, fbvecs = dpd.get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = grad.gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = sims.multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[10, 90], snr=SNR)
sfmodel = sfm.SparseFascicleModel(gtab, response=[0.0015, 0.0003, 0.0003])
sffit = sfmodel.fit(S)
pred = sffit.predict()
npt.assert_(xval.coeff_of_determination(pred, S) > 97)
# Should be possible to predict using a different gtab:
new_gtab = grad.gradient_table(bvals[::2], bvecs[::2])
new_pred = sffit.predict(new_gtab)
npt.assert_(xval.coeff_of_determination(new_pred, S[::2]) > 97)
def _create_mt_sim(mevals, angles, fractions, S0, SNR, half_sphere=False):
_, fbvals, fbvecs = get_data('small_64D')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=fractions, snr=SNR)
sphere = get_sphere('symmetric724').subdivide(2)
if half_sphere:
sphere = HemiSphere.from_sphere(sphere)
odf_gt = multi_tensor_odf(sphere.vertices, mevals,
angles=angles, fractions=fractions)
return odf_gt, sticks, sphere
def test_fwdti_singlevoxel():
# Simulation when water contamination is added
gtf = 0.44444 # ground truth volume fraction
mevals = np.array([[0.0017, 0.0003, 0.0003], [0.003, 0.003, 0.003]])
S_conta, peaks = multi_tensor(gtab_2s, mevals, S0=100,
angles=[(90, 0), (90, 0)],
fractions=[(1-gtf) * 100, gtf*100], snr=None)
fwdm = fwdti.FreeWaterTensorModel(gtab_2s, 'WLS')
fwefit = fwdm.fit(S_conta)
FAfwe = fwefit.fa
Ffwe = fwefit.f
MDfwe = fwefit.md
assert_almost_equal(FAdti, FAfwe, decimal=3)
assert_almost_equal(Ffwe, gtf, decimal=3)
assert_almost_equal(MDfwe, MDdti, decimal=3)
# Test non-linear fit
fwdm = fwdti.FreeWaterTensorModel(gtab_2s, 'NLS', cholesky=False)
fwefit = fwdm.fit(S_conta)
FAfwe = fwefit.fa
Ffwe = fwefit.f
MDfwe = fwefit.md
assert_almost_equal(FAdti, FAfwe)
assert_almost_equal(Ffwe, gtf)
assert_almost_equal(MDfwe, MDdti)
# Test cholesky
fwdm = fwdti.FreeWaterTensorModel(gtab_2s, 'NLS', cholesky=True)
fwefit = fwdm.fit(S_conta)
FAfwe = fwefit.fa
Ffwe = fwefit.f
MDfwe = fwefit.md
assert_almost_equal(FAdti, FAfwe)
assert_almost_equal(Ffwe, gtf)
assert_almost_equal(MDfwe, MDfwe)
def test_r2_term_odf_sharp():
SNR = None
S0 = 1
angle = 45 # 45 degrees is a very tight angle to disentangle
_, fbvals, fbvecs = get_fnames('small_64D') # get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
sphere = default_sphere
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (angle, 0)]
S, _ = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
odfs_sh = sf_to_sh(odf_gt, sphere, sh_order=8, basis_type=None)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
fodf_sh = odf_sh_to_sharp(odfs_sh,
sphere,
basis=None,
ratio=3 / 15.,
sh_order=8,
lambda_=1.,
tau=0.1,
r2_term=True)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
fodf = sh_to_sf(fodf_sh, sphere, sh_order=8, basis_type=None)
directions_gt, _, _ = peak_directions(odf_gt, sphere)
directions, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions_gt, directions)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
# This should pass as well
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
sdt_model = ConstrainedSDTModel(gtab, ratio=3 / 15., sh_order=8)
sdt_fit = sdt_model.fit(S)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
fodf = sdt_fit.odf(sphere)
directions_gt, _, _ = peak_directions(odf_gt, sphere)
directions, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions_gt, directions)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
def test_csd_predict():
"""
Test prediction API
"""
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, _ = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
sphere = small_sphere
multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
response = (np.array([0.0015, 0.0003, 0.0003]), S0)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(S)
# Predicting from a fit should give the same result as predicting from a
# model, S0 is 1 by default
prediction1 = csd_fit.predict()
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
prediction2 = csd.predict(csd_fit.shm_coeff)
npt.assert_array_equal(prediction1, prediction2)
npt.assert_array_equal(prediction1[..., gtab.b0s_mask], 1.)
# Same with a different S0
prediction1 = csd_fit.predict(S0=123.)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
prediction2 = csd.predict(csd_fit.shm_coeff, S0=123.)
npt.assert_array_equal(prediction1, prediction2)
npt.assert_array_equal(prediction1[..., gtab.b0s_mask], 123.)
# For "well behaved" coefficients, the model should be able to find the
# coefficients from the predicted signal.
coeff = np.random.random(csd_fit.shm_coeff.shape) - .5
coeff[..., 0] = 10.
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
S = csd.predict(coeff)
csd_fit = csd.fit(S)
npt.assert_array_almost_equal(coeff, csd_fit.shm_coeff)
# Test predict on nd-data set
S_nd = np.zeros((2, 3, 4, S.size))
S_nd[:] = S
fit = csd.fit(S_nd)
predict1 = fit.predict()
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
predict2 = csd.predict(fit.shm_coeff)
npt.assert_array_almost_equal(predict1, predict2)
def test_recursive_response_calibration():
"""
Test the recursive response calibration method.
"""
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
sphere = default_sphere
gtab = gradient_table(bvals, bvecs)
evals = np.array([0.0015, 0.0003, 0.0003])
evecs = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]]).T
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
where_dwi = lazy_index(~gtab.b0s_mask)
S_cross, _ = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
S_single = single_tensor(gtab, S0, evals, evecs, snr=SNR)
data = np.concatenate((np.tile(S_cross, (8, 1)), np.tile(S_single,
(2, 1))),
axis=0)
odf_gt_cross = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
odf_gt_single = single_tensor_odf(sphere.vertices, evals, evecs)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
response = recursive_response(gtab,
data,
mask=None,
sh_order=8,
peak_thr=0.01,
init_fa=0.05,
init_trace=0.0021,
iter=8,
convergence=0.001,
parallel=False)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(data)
assert_equal(np.all(csd_fit.shm_coeff[:, 0] >= 0), True)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
fodf = csd_fit.odf(sphere)
directions_gt_single, _, _ = peak_directions(odf_gt_single, sphere)
directions_gt_cross, _, _ = peak_directions(odf_gt_cross, sphere)
directions_single, _, _ = peak_directions(fodf[8, :], sphere)
directions_cross, _, _ = peak_directions(fodf[0, :], sphere)
ang_sim = angular_similarity(directions_cross, directions_gt_cross)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions_cross.shape[0], 2)
assert_equal(directions_gt_cross.shape[0], 2)
ang_sim = angular_similarity(directions_single, directions_gt_single)
assert_equal(ang_sim > 0.9, True)
assert_equal(directions_single.shape[0], 1)
assert_equal(directions_gt_single.shape[0], 1)
with warnings.catch_warnings(record=True) as w:
sphere = Sphere(xyz=gtab.gradients[where_dwi])
npt.assert_equal(len(w), 1)
npt.assert_(issubclass(w[0].category, UserWarning))
npt.assert_("Vertices are not on the unit sphere" in str(w[0].message))
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=descoteaux07_legacy_msg,
category=PendingDeprecationWarning)
sf = response.on_sphere(sphere)
S = np.concatenate(([response.S0], sf))
tenmodel = TensorModel(gtab, min_signal=0.001)
tenfit = tenmodel.fit(S)
FA = fractional_anisotropy(tenfit.evals)
FA_gt = fractional_anisotropy(evals)
assert_almost_equal(FA, FA_gt, 1)
# Matrix where synthetic signals will be stored
dwi = np.empty((f.size, ang.size, bvals.size))
for f_i in range(f.size):
# estimating volume fractions for individual tensors
fractions = np.array([100 - f[f_i], f[f_i], 100 - f[f_i], f[f_i]]) * 0.5
for a_i in range(ang.size):
# defining the directions for individual tensors
angles = [(ang[a_i], 0.0), (ang[a_i], 0.0), (0.0, 0.0), (0.0, 0.0)]
# producing signals using Dipy's function multi_tensor
signal, sticks = multi_tensor(gtab,
mevals,
S0=100,
angles=angles,
fractions=fractions,
snr=None)
dwi[f_i, a_i, :] = signal
"""
Now that all synthetic signals were produced, we can go forward with
MSDKI fitting. As other Dipy's reconstruction techniques, the MSDKI model has
to be first defined for the specific GradientTable object of the synthetic
data. For MSDKI, this is done by instantiating the MeanDiffusionKurtosisModel
object in the following way:
"""
msdki_model = msdki.MeanDiffusionKurtosisModel(gtab)
"""
MSDKI can then be fitted to the synthetic data by calling the ``fit`` function
of this object:
def test_peaks_shm_coeff():
SNR = 100
S0 = 100
_, fbvals, fbvecs = get_data('small_64D')
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
bvals = np.load(fbvals)
bvecs = np.load(fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
data, _ = multi_tensor(gtab,
mevals,
S0,
angles=[(0, 0), (60, 0)],
fractions=[50, 50],
snr=SNR)
from dipy.reconst.shm import CsaOdfModel
model = CsaOdfModel(gtab, 4)
pam = peaks_from_model(model,
data[None, :],
sphere,
.5,
45,
return_odf=True,
return_sh=True)
# Test that spherical harmonic coefficients return back correctly
B = np.linalg.pinv(pam.invB)
odf2 = np.dot(pam.shm_coeff, B)
assert_array_almost_equal(pam.odf, odf2)
assert_equal(pam.shm_coeff.shape[-1], 45)
pam = peaks_from_model(model,
data[None, :],
sphere,
.5,
45,
return_odf=True,
return_sh=False)
assert_equal(pam.shm_coeff, None)
pam = peaks_from_model(model,
data[None, :],
sphere,
.5,
45,
return_odf=True,
return_sh=True,
sh_basis_type='mrtrix')
B = np.linalg.pinv(pam.invB)
odf2 = np.dot(pam.shm_coeff, B)
assert_array_almost_equal(pam.odf, odf2)
def setup_module():
global gtab, ivim_fit_single, ivim_model_trr, data_single, params_trr, \
data_multi, ivim_params_trr, D_star, D, f, S0, gtab_with_multiple_b0, \
noisy_single, mevals, gtab_no_b0, ivim_fit_multi, ivim_model_VP, \
f_VP, D_star_VP, D_VP, params_VP
# Let us generate some data for testing.
bvals = np.array([
0., 10., 20., 30., 40., 60., 80., 100., 120., 140., 160., 180., 200.,
300., 400., 500., 600., 700., 800., 900., 1000.
])
N = len(bvals)
bvecs = generate_bvecs(N)
gtab = gradient_table(bvals, bvecs.T, b0_threshold=0)
S0, f, D_star, D = 1000.0, 0.132, 0.00885, 0.000921
# params for a single voxel
params_trr = np.array([S0, f, D_star, D])
mevals = np.array(([D_star, D_star, D_star], [D, D, D]))
# This gives an isotropic signal.
signal = multi_tensor(gtab,
mevals,
snr=None,
S0=S0,
fractions=[f * 100, 100 * (1 - f)])
# Single voxel data
data_single = signal[0]
data_multi = np.zeros((2, 2, 1, len(gtab.bvals)))
data_multi[0, 0,
0] = data_multi[0, 1,
0] = data_multi[1, 0,
0] = data_multi[1, 1,
0] = data_single
ivim_params_trr = np.zeros((2, 2, 1, 4))
ivim_params_trr[0, 0, 0] = ivim_params_trr[0, 1, 0] = params_trr
ivim_params_trr[1, 0, 0] = ivim_params_trr[1, 1, 0] = params_trr
ivim_model_trr = IvimModel(gtab, fit_method='trr')
ivim_model_one_stage = IvimModel(gtab, fit_method='trr')
ivim_fit_single = ivim_model_trr.fit(data_single)
ivim_fit_multi = ivim_model_trr.fit(data_multi)
ivim_model_one_stage.fit(data_single)
ivim_model_one_stage.fit(data_multi)
bvals_no_b0 = np.array([
5., 10., 20., 30., 40., 60., 80., 100., 120., 140., 160., 180., 200.,
300., 400., 500., 600., 700., 800., 900., 1000.
])
_ = generate_bvecs(N) # bvecs_no_b0
gtab_no_b0 = gradient_table(bvals_no_b0, bvecs.T, b0_threshold=0)
bvals_with_multiple_b0 = np.array([
0., 0., 0., 0., 40., 60., 80., 100., 120., 140., 160., 180., 200.,
300., 400., 500., 600., 700., 800., 900., 1000.
])
bvecs_with_multiple_b0 = generate_bvecs(N)
gtab_with_multiple_b0 = gradient_table(bvals_with_multiple_b0,
bvecs_with_multiple_b0.T,
b0_threshold=0)
noisy_single = np.array([
4243.71728516, 4317.81298828, 4244.35693359, 4439.36816406,
4420.06201172, 4152.30078125, 4114.34912109, 4104.59375, 4151.61914062,
4003.58374023, 4013.68408203, 3906.39428711, 3909.06079102,
3495.27197266, 3402.57006836, 3163.10180664, 2896.04003906,
2663.7253418, 2614.87695312, 2316.55371094, 2267.7722168
])
noisy_multi = np.zeros((2, 2, 1, len(gtab.bvals)))
noisy_multi[0, 1, 0] = noisy_multi[1, 0, 0] = noisy_multi[1, 1,
0] = noisy_single
noisy_multi[0, 0, 0] = data_single
ivim_model_VP = IvimModel(gtab, fit_method='VarPro')
f_VP, D_star_VP, D_VP = 0.13, 0.0088, 0.000921
# params for a single voxel
params_VP = np.array([f, D_star, D])
ivim_params_VP = np.zeros((2, 2, 1, 3))
ivim_params_VP[0, 0, 0] = ivim_params_VP[0, 1, 0] = params_VP
ivim_params_VP[1, 0, 0] = ivim_params_VP[1, 1, 0] = params_VP
def test_peaksFromModelParallel():
SNR = 100
S0 = 100
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
data, _ = multi_tensor(gtab,
mevals,
S0,
angles=[(0, 0), (60, 0)],
fractions=[50, 50],
snr=SNR)
for sphere in [_sphere, default_sphere]:
# test equality with/without multiprocessing
model = SimpleOdfModel(gtab)
pam_multi = peaks_from_model(model,
data,
sphere,
.5,
45,
normalize_peaks=True,
return_odf=True,
return_sh=True,
parallel=True)
pam_single = peaks_from_model(model,
data,
sphere,
.5,
45,
normalize_peaks=True,
return_odf=True,
return_sh=True,
parallel=False)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", category=UserWarning)
pam_multi_inv1 = peaks_from_model(model,
data,
sphere,
.5,
45,
normalize_peaks=True,
return_odf=True,
return_sh=True,
parallel=True,
nbr_processes=0)
pam_multi_inv2 = peaks_from_model(model,
data,
sphere,
.5,
45,
normalize_peaks=True,
return_odf=True,
return_sh=True,
parallel=True,
nbr_processes=-2)
assert_(len(w) == 2)
assert_(issubclass(w[0].category, UserWarning))
assert_(issubclass(w[1].category, UserWarning))
assert_("Invalid number of processes " in str(w[0].message))
assert_("Invalid number of processes " in str(w[1].message))
for pam in [pam_multi, pam_multi_inv1, pam_multi_inv2]:
assert_equal(pam.gfa.dtype, pam_single.gfa.dtype)
assert_equal(pam.gfa.shape, pam_single.gfa.shape)
assert_array_almost_equal(pam.gfa, pam_single.gfa)
assert_equal(pam.qa.dtype, pam_single.qa.dtype)
assert_equal(pam.qa.shape, pam_single.qa.shape)
assert_array_almost_equal(pam.qa, pam_single.qa)
assert_equal(pam.peak_values.dtype,
pam_single.peak_values.dtype)
assert_equal(pam.peak_values.shape,
pam_single.peak_values.shape)
assert_array_almost_equal(pam.peak_values,
pam_single.peak_values)
assert_equal(pam.peak_indices.dtype,
pam_single.peak_indices.dtype)
assert_equal(pam.peak_indices.shape,
pam_single.peak_indices.shape)
assert_array_equal(pam.peak_indices, pam_single.peak_indices)
assert_equal(pam.peak_dirs.dtype, pam_single.peak_dirs.dtype)
assert_equal(pam.peak_dirs.shape, pam_single.peak_dirs.shape)
assert_array_almost_equal(pam.peak_dirs, pam_single.peak_dirs)
assert_equal(pam.shm_coeff.dtype, pam_single.shm_coeff.dtype)
assert_equal(pam.shm_coeff.shape, pam_single.shm_coeff.shape)
assert_array_almost_equal(pam.shm_coeff, pam_single.shm_coeff)
assert_equal(pam.odf.dtype, pam_single.odf.dtype)
assert_equal(pam.odf.shape, pam_single.odf.shape)
assert_array_almost_equal(pam.odf, pam_single.odf)
def rfiw_phantom(gtab, snr=None):
"""rectangle fiber immersed in water"""
# define voxel index
slice_ind = np.zeros((10, 10, 8))
slice_ind[4:7, 4:7, :] = 1
slice_ind[4:7, 7, :] = 2
slice_ind[7, 7, :] = 3
slice_ind[7, 4:7, :] = 4
slice_ind[7, 3, :] = 5
slice_ind[4:7, 3, :] = 6
slice_ind[3, 3, :] = 7
slice_ind[3, 4:7, :] = 8
slice_ind[3, 7, :] = 9
# Define tissue diffusion parameters
# Restricted diffusion
ADr = 0.99e-3
RDr = 0.0
# Hindered diffusion
ADh = 2.26e-3
RDh = 0.87e-3
# S0 value for tissue
S1 = 50
# Fraction between Restricted and Hindered diffusion
fia = 0.51
# Define water diffusion
Dwater = 3e-3
S2 = 100 # S0 value for water
# Define tissue volume fraction for each voxel type (in index order)
f = np.array([0., 1., 0.6, 0.18, 0.30, 0.15, 0.50, 0.35, 0.70, 0.42])
# Define S0 for each voxel (in index order)
S0 = S1 * f + S2 * (1 - f)
# multi tensor simulations assume that each water pull as constant S0
# since I am assuming that tissue and water voxels have different S0,
# tissue volume fractions have to be adjusted to the measured f values when
# constant S0 are assumed constant. Doing this correction, simulations will
# be analogous to simulates that S0 are different for each media. (For more
# details on this contact the phantom designer)
f1 = f * S1 / S0
mevals = np.array([[ADr, RDr, RDr], [ADh, RDh, RDh],
[Dwater, Dwater, Dwater]])
angles = [(0, 0, 1), (0, 0, 1), (0, 0, 1)]
dwi = np.zeros(slice_ind.shape + (gtab.bvals.size, ))
for i in range(10):
fractions = [f1[i] * fia * 100, f1[i] *
(1 - fia) * 100, (1 - f1[i]) * 100]
sig, direction = multi_tensor(gtab, mevals, S0=S0[i], angles=angles,
fractions=fractions, snr=None)
dwi[slice_ind == i, :] = sig
if snr is None:
return dwi
else:
sigma = S2 * 1.0 / snr
n1 = np.random.normal(0, sigma, size=dwi.shape)
n2 = np.random.normal(0, sigma, size=dwi.shape)
return [np.sqrt((dwi / np.sqrt(2) + n1)**2 +
(dwi / np.sqrt(2) + n2)**2), sigma]
def test_peaksFromModelParallel():
SNR = 100
S0 = 100
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
data, _ = multi_tensor(gtab, mevals, S0, angles=[(0, 0), (60, 0)],
fractions=[50, 50], snr=SNR)
for sphere in [_sphere, default_sphere]:
# test equality with/without multiprocessing
model = SimpleOdfModel(gtab)
pam_multi = peaks_from_model(model, data, sphere, .5, 45,
normalize_peaks=True, return_odf=True,
return_sh=True, parallel=True)
pam_single = peaks_from_model(model, data, sphere, .5, 45,
normalize_peaks=True, return_odf=True,
return_sh=True, parallel=False)
pam_multi_inv1 = peaks_from_model(model, data, sphere, .5, 45,
normalize_peaks=True,
return_odf=True,
return_sh=True, parallel=True,
nbr_processes=-1)
pam_multi_inv2 = peaks_from_model(model, data, sphere, .5, 45,
normalize_peaks=True,
return_odf=True,
return_sh=True, parallel=True,
nbr_processes=-2)
for pam in [pam_multi, pam_multi_inv1, pam_multi_inv2]:
assert_equal(pam.gfa.dtype, pam_single.gfa.dtype)
assert_equal(pam.gfa.shape, pam_single.gfa.shape)
assert_array_almost_equal(pam.gfa, pam_single.gfa)
assert_equal(pam.qa.dtype, pam_single.qa.dtype)
assert_equal(pam.qa.shape, pam_single.qa.shape)
assert_array_almost_equal(pam.qa, pam_single.qa)
assert_equal(pam.peak_values.dtype,
pam_single.peak_values.dtype)
assert_equal(pam.peak_values.shape,
pam_single.peak_values.shape)
assert_array_almost_equal(pam.peak_values,
pam_single.peak_values)
assert_equal(pam.peak_indices.dtype,
pam_single.peak_indices.dtype)
assert_equal(pam.peak_indices.shape,
pam_single.peak_indices.shape)
assert_array_equal(pam.peak_indices, pam_single.peak_indices)
assert_equal(pam.peak_dirs.dtype, pam_single.peak_dirs.dtype)
assert_equal(pam.peak_dirs.shape, pam_single.peak_dirs.shape)
assert_array_almost_equal(pam.peak_dirs, pam_single.peak_dirs)
assert_equal(pam.shm_coeff.dtype, pam_single.shm_coeff.dtype)
assert_equal(pam.shm_coeff.shape, pam_single.shm_coeff.shape)
assert_array_almost_equal(pam.shm_coeff, pam_single.shm_coeff)
assert_equal(pam.odf.dtype, pam_single.odf.dtype)
assert_equal(pam.odf.shape, pam_single.odf.shape)
assert_array_almost_equal(pam.odf, pam_single.odf)
RDe = RDE[i, j, k]
fie = FIE[i, j, k]
mevals = np.array([[ADi, RDi, RDi], [ADe, RDe, RDe]])
frac = [fie * 100, (1 - fie) * 100]
theta = random.uniform(0, 180)
phi = random.uniform(0, 320)
angles = [(theta, phi), (theta, phi)]
signal, dt, kt = multi_tensor_dki(gtab_2s,
mevals,
angles=angles,
fractions=frac,
snr=None)
DWIsim[i, j, k, :] = signal
signal, sticks = multi_tensor(gtab_2s,
mevals,
angles=angles,
fractions=frac,
snr=None)
DWIsim_all_taylor[i, j, k, :] = signal
def test_single_fiber_model():
# single fiber simulate (which is the assumption of our model)
fie = 0.49
ADi = 0.00099
ADe = 0.00226
RDi = 0
RDe = 0.00087
# prepare simulation:
theta = random.uniform(0, 180)
def test_shore_metrics():
gtab = get_gtab_taiwan_dsi()
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angl = [(0, 0), (60, 0)]
S, _ = multi_tensor(gtab, mevals, S0=100.0, angles=angl,
fractions=[50, 50], snr=None)
# test shore_indices
n = 7
l = 6
m = -4
radial_order, c = shore_order(n, l, m)
n2, l2, m2 = shore_indices(radial_order, c)
npt.assert_equal(n, n2)
npt.assert_equal(l, l2)
npt.assert_equal(m, m2)
radial_order = 6
c = 41
n, l, m = shore_indices(radial_order, c)
radial_order2, c2 = shore_order(n, l, m)
npt.assert_equal(radial_order, radial_order2)
npt.assert_equal(c, c2)
npt.assert_raises(ValueError, shore_indices, 6, 100)
npt.assert_raises(ValueError, shore_order, m, n, l)
# since we are testing without noise we can use higher order and lower
# lambdas, with respect to the default.
radial_order = 8
zeta = 700
lambdaN = 1e-12
lambdaL = 1e-12
asm = ShoreModel(gtab, radial_order=radial_order,
zeta=zeta, lambdaN=lambdaN, lambdaL=lambdaL)
asmfit = asm.fit(S)
c_shore = asmfit.shore_coeff
cmat = shore_matrix(radial_order, zeta, gtab)
S_reconst = np.dot(cmat, c_shore)
# test the signal reconstruction
S = S / S[0]
nmse_signal = np.sqrt(np.sum((S - S_reconst) ** 2)) / (S.sum())
npt.assert_almost_equal(nmse_signal, 0.0, 4)
# test if the analytical integral of the pdf is equal to one
integral = 0
for n in range(int((radial_order)/2 + 1)):
integral += c_shore[n] * (np.pi**(-1.5) * zeta ** (-1.5) *
genlaguerre(n, 0.5)(0)) ** 0.5
npt.assert_almost_equal(integral, 1.0, 10)
# test if the integral of the pdf calculated on a discrete grid is
# equal to one
pdf_discrete = asmfit.pdf_grid(17, 40e-3)
integral = pdf_discrete.sum()
npt.assert_almost_equal(integral, 1.0, 1)
# compare the shore pdf with the ground truth multi_tensor pdf
sphere = get_sphere('symmetric724')
v = sphere.vertices
radius = 10e-3
pdf_shore = asmfit.pdf(v * radius)
pdf_mt = multi_tensor_pdf(v * radius, mevals=mevals,
angles=angl, fractions=[50, 50])
nmse_pdf = np.sqrt(np.sum((pdf_mt - pdf_shore) ** 2)) / (pdf_mt.sum())
npt.assert_almost_equal(nmse_pdf, 0.0, 2)
# compare the shore rtop with the ground truth multi_tensor rtop
rtop_shore_signal = asmfit.rtop_signal()
rtop_shore_pdf = asmfit.rtop_pdf()
npt.assert_almost_equal(rtop_shore_signal, rtop_shore_pdf, 9)
rtop_mt = multi_tensor_rtop([.5, .5], mevals=mevals)
npt.assert_equal(rtop_mt / rtop_shore_signal < 1.10 and
rtop_mt / rtop_shore_signal > 0.95, True)
# compare the shore msd with the ground truth multi_tensor msd
msd_mt = multi_tensor_msd([.5, .5], mevals=mevals)
msd_shore = asmfit.msd()
npt.assert_equal(msd_mt / msd_shore < 1.05 and msd_mt / msd_shore > 0.95,
True)
def test_csdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs, b0_threshold=0)
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
response = (np.array([0.0015, 0.0003, 0.0003]), S0)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(S)
assert_equal(csd_fit.shm_coeff[0] > 0, True)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", category=UserWarning)
_ = ConstrainedSphericalDeconvModel(gtab, response, sh_order=10)
assert_greater(len([lw for lw in w if issubclass(lw.category,
UserWarning)]), 0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", category=UserWarning)
ConstrainedSphericalDeconvModel(gtab, response, sh_order=8)
assert_equal(len([lw for lw in w if issubclass(lw.category,
UserWarning)]), 0)
mevecs = []
for s in sticks:
mevecs += [all_tensor_evecs(s).T]
S2 = single_tensor(gtab, 100, mevals[0], mevecs[0], snr=None)
big_S = np.zeros((10, 10, 10, len(S2)))
big_S[:] = S2
aresponse, aratio = auto_response(gtab, big_S, roi_center=(5, 5, 4),
roi_radius=3, fa_thr=0.5)
assert_array_almost_equal(aresponse[0], response[0])
assert_almost_equal(aresponse[1], 100)
assert_almost_equal(aratio, response[0][1] / response[0][0])
auto_response(gtab, big_S, roi_radius=3, fa_thr=0.5)
assert_array_almost_equal(aresponse[0], response[0])
_, _, nvoxels = auto_response(gtab, big_S, roi_center=(5, 5, 4),
roi_radius=30, fa_thr=0.5,
return_number_of_voxels=True)
assert_equal(nvoxels, 1000)
_, _, nvoxels = auto_response(gtab, big_S, roi_center=(5, 5, 4),
roi_radius=30, fa_thr=1,
return_number_of_voxels=True)
assert_equal(nvoxels, 0)
# repetitions for the given pair of minimum-maximun
# b-value
rep_simulates = np.zeros((nDTdirs * nrep, bvecs.shape[0]))
# Repeat simulations for the 120 diffusion gradient directions
for di in range(nDTdirs):
d = DTdirs[di]
# Repeat each direction 100 times
for s_i in np.arange(di * nrep, (di + 1) * nrep):
# Multi-compartmental simulations are done using
# Dipy's function multi_tensor
signal, sticks = multi_tensor(gtab,
mevals,
S0=100,
angles=[d, (1, 0, 0)],
fractions=fractions,
snr=SNRa)
rep_simulates[s_i, :] = signal
# Process NLS fitting for all simulation repetitions of
# a given pair of minimum-maximun b-value
fw_params[bmin_i,
bmax_i, :, :] = nls_fit_tensor(gtab, rep_simulates)
# Process computing progress
prog = (bmax_i * 1.0) / bmax.size + (bmin_i + 1.0) / (bmax.size *
bmin.size)
time.sleep(1)
sys.stdout.write("\r%f%%" % prog * 100)
sys.stdout.flush()
# Let us generate some data for testing.
bvals = np.array([0., 10., 20., 30., 40., 60., 80., 100.,
120., 140., 160., 180., 200., 300., 400.,
500., 600., 700., 800., 900., 1000.])
N = len(bvals)
bvecs = generate_bvecs(N)
gtab = gradient_table(bvals, bvecs.T)
S0, f, D_star, D = 1000.0, 0.132, 0.00885, 0.000921
# params for a single voxel
params = np.array([S0, f, D_star, D])
mevals = np.array(([D_star, D_star, D_star], [D, D, D]))
# This gives an isotropic signal.
signal = multi_tensor(gtab, mevals, snr=None, S0=S0,
fractions=[f * 100, 100 * (1 - f)])
# Single voxel data
data_single = signal[0]
data_multi = np.zeros((2, 2, 1, len(gtab.bvals)))
data_multi[0, 0, 0] = data_multi[0, 1, 0] = data_multi[
1, 0, 0] = data_multi[1, 1, 0] = data_single
ivim_params = np.zeros((2, 2, 1, 4))
ivim_params[0, 0, 0] = ivim_params[0, 1, 0] = params
ivim_params[1, 0, 0] = ivim_params[1, 1, 0] = params
ivim_model = IvimModel(gtab)
ivim_model_one_stage = IvimModel(gtab)
ivim_fit_single = ivim_model.fit(data_single)
ivim_fit_multi = ivim_model.fit(data_multi)
FAref = np.zeros((2, 2, 2))
MDref = np.zeros((2, 2, 2))
# Diffusion of tissue and water compartments are constant for all voxel
mevals = np.array([[0.0017, 0.0003, 0.0003], [0.003, 0.003, 0.003]])
# volume fractions
GTF = np.array([[[0.06, 0.71], [0.33, 0.91]], [[0., 0.], [0., 0.]]])
# S0 multivoxel
S0m = 100 * np.ones((2, 2, 2))
# model_params ground truth (to be fill)
model_params_mv = np.zeros((2, 2, 2, 13))
for i in range(2):
for j in range(2):
gtf = GTF[0, i, j]
S, p = multi_tensor(gtab_2s,
mevals,
S0=100,
angles=[(90, 0), (90, 0)],
fractions=[(1 - gtf) * 100, gtf * 100],
snr=None)
DWI[0, i, j] = S
FAref[0, i, j] = FAdti
MDref[0, i, j] = MDdti
R = all_tensor_evecs(p[0])
R = R.reshape((9))
model_params_mv[0, i, j] = np.concatenate(
([0.0017, 0.0003, 0.0003], R, [gtf]), axis=0)
def test_fwdti_singlevoxel():
# Simulation when water contamination is added
gtf = 0.44444 # ground truth volume fraction
mevals = np.array([[0.0017, 0.0003, 0.0003], [0.003, 0.003, 0.003]])
def test_odfdeconv():
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
S, _ = multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[50, 50],
snr=SNR)
sphere = get_sphere('symmetric362')
odf_gt = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
e1 = 15.0
e2 = 3.0
ratio = e2 / e1
csd = ConstrainedSDTModel(gtab, ratio, None)
csd_fit = csd.fit(S)
fodf = csd_fit.odf(sphere)
directions, _, _ = peak_directions(odf_gt, sphere)
directions2, _, _ = peak_directions(fodf, sphere)
ang_sim = angular_similarity(directions, directions2)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions.shape[0], 2)
assert_equal(directions2.shape[0], 2)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=10)
w_count = len(w)
# A warning is expected from the ConstrainedSDTModel constructor
# and additionnal warnings should be raised where legacy SH bases
# are used
assert_equal(w_count > 1, True)
with warnings.catch_warnings(record=True) as w:
ConstrainedSDTModel(gtab, ratio, sh_order=8)
# Test that the warning from ConstrainedSDTModel
# constructor is no more raised
assert_equal(len(w) == w_count - 1, True)
csd_fit = csd.fit(np.zeros_like(S))
fodf = csd_fit.odf(sphere)
assert_array_equal(fodf, np.zeros_like(fodf))
odf_sh = np.zeros_like(fodf)
odf_sh[1] = np.nan
fodf, _ = odf_deconv(odf_sh, csd.R, csd.B_reg)
assert_array_equal(fodf, np.zeros_like(fodf))
def test_ivim_tensor():
bvals = array([
10., 40., 60., 80., 100., 150., 200., 300., 500., 700., 800., 900.,
1000., 10., 40., 60., 80., 100., 150., 200., 300., 500., 700., 800.,
900., 1000., 10., 40., 60., 80., 100., 150., 200., 300., 500., 700.,
800., 900., 1000., 10., 40., 60., 80., 100., 150., 200., 300., 500.,
700., 800., 900., 1000., 10., 40., 60., 80., 100., 150., 200., 300.,
500., 700., 800., 900., 1000., 10., 40., 60., 80., 100., 150., 200.,
300., 500., 700., 800., 900., 1000., 0.
])
bvecs = array([[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[-1.00000e+00, -3.40515e-09, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[3.40515e-09, 1.00000e+00, 0.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[0.00000e+00, 0.00000e+00, 1.00000e+00],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[7.04358e-01, -8.80947e-02, -7.04358e-01],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-7.04358e-01, 7.04358e-01, 8.80947e-02],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[-8.80947e-02, 7.04358e-01, 7.04358e-01],
[0.00000e+00, 0.00000e+00, 0.00000e+00]])
gtab = gradient_table(bvals, bvecs, b0_threshold=0)
mevals = np.array([[0.001, 0.0005, 0.0005], [0.1, 0.01, 0.01]])
itm = IvimTensorModel(gtab)
betas = np.arange(0.05, 0.3, 0.05)
for ii in range(len(betas)):
sim = multi_tensor(gtab,
mevals=mevals,
snr=100,
fractions=[100 * (1 - betas[ii]),
betas[ii] * 100])[0]
itf = itm.fit(np.array([sim]))
assert np.allclose(itf.perfusion_fraction, betas[ii], atol=1e-2)
prediction = itf.predict(gtab)
assert np.allclose(prediction, sim, atol=0.05)
def test_bootstap_peak_tracker():
"""This tests that the Bootstrat Peak Direction Getter plays nice
LocalTracking and produces reasonable streamlines in a simple example.
"""
sphere = get_sphere('repulsion100')
# A simple image with three possible configurations, a vertical tract,
# a horizontal tract and a crossing
simple_image = np.array([
[0, 1, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0],
[2, 3, 2, 2, 2, 0],
[0, 1, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0],
])
simple_image = simple_image[..., None]
bvecs = sphere.vertices
bvals = np.ones(len(bvecs)) * 1000
bvecs = np.insert(bvecs, 0, np.array([0, 0, 0]), axis=0)
bvals = np.insert(bvals, 0, 0)
gtab = gradient_table(bvals, bvecs)
angles = [(90, 90), (90, 0)]
fracs = [50, 50]
mevals = np.array([[1.5, 0.4, 0.4], [1.5, 0.4, 0.4]]) * 1e-3
mevecs = [
np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]])
]
voxel1 = single_tensor(gtab, 1, mevals[0], mevecs[0], snr=None)
voxel2 = single_tensor(gtab, 1, mevals[0], mevecs[1], snr=None)
voxel3, _ = multi_tensor(gtab,
mevals,
fractions=fracs,
angles=angles,
snr=None)
data = np.tile(voxel3, [5, 6, 1, 1])
data[simple_image == 1] = voxel1
data[simple_image == 2] = voxel2
response = (np.array(mevals[1]), 1)
csd_model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=6)
seeds = [np.array([0., 1., 0.]), np.array([2., 4., 0.])]
tc = BinaryTissueClassifier((simple_image > 0).astype(float))
boot_dg = BootDirectionGetter.from_data(data, csd_model, 60)
streamlines_generator = LocalTracking(boot_dg, tc, seeds, np.eye(4), 1.)
streamlines = Streamlines(streamlines_generator)
expected = [
np.array([[0., 1., 0.], [1., 1., 0.], [2., 1., 0.], [3., 1., 0.],
[4., 1., 0.]]),
np.array([
[2., 5., 0.],
[2., 4., 0.],
[2., 3., 0.],
[2., 2., 0.],
[2., 1., 0.],
[2., 0., 0.],
])
]
def allclose(x, y):
return x.shape == y.shape and np.allclose(x, y, atol=0.5)
if not allclose(streamlines[0], expected[0]):
raise AssertionError()
if not allclose(streamlines[1], expected[1]):
raise AssertionError()
def test_predict():
SNR = 1000
S0 = 100
_, fbvals, fbvecs = dpd.get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
gtab = grad.gradient_table(bvals, bvecs)
mevals = np.array(([0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (60, 0)]
S, sticks = sims.multi_tensor(gtab,
mevals,
S0,
angles=angles,
fractions=[10, 90],
snr=SNR)
sfmodel = sfm.SparseFascicleModel(gtab, response=[0.0015, 0.0003, 0.0003])
sffit = sfmodel.fit(S)
pred = sffit.predict()
npt.assert_(xval.coeff_of_determination(pred, S) > 97)
# Should be possible to predict using a different gtab:
new_gtab = grad.gradient_table(bvals[::2], bvecs[::2])
new_pred = sffit.predict(new_gtab)
npt.assert_(xval.coeff_of_determination(new_pred, S[::2]) > 97)
# Should be possible to predict for a single direction:
new_gtab = grad.gradient_table(bvals[1][None], bvecs[1][None, :])
new_pred = sffit.predict(new_gtab)
# Fitting and predicting with a volume of data:
fdata, fbval, fbvec = dpd.get_fnames('small_25')
gtab = grad.gradient_table(fbval, fbvec)
data = load_nifti_data(fdata)
sfmodel = sfm.SparseFascicleModel(gtab, response=[0.0015, 0.0003, 0.0003])
sffit = sfmodel.fit(data)
pred = sffit.predict()
# Should be possible to predict using a different gtab:
new_gtab = grad.gradient_table(bvals[::2], bvecs[::2])
new_pred = sffit.predict(new_gtab)
npt.assert_equal(
new_pred.shape,
data.shape[:-1] + bvals[::2].shape,
)
# Should be possible to predict for a single direction:
new_gtab = grad.gradient_table(bvals[1][None], bvecs[1][None, :])
new_pred = sffit.predict(new_gtab)
npt.assert_equal(new_pred.shape, data.shape[:-1])
# Fitting and predicting with masked data:
mask = np.zeros(data.shape[:3])
mask[2:5, 2:5, :] = 1
sffit = sfmodel.fit(data, mask=mask)
pred = sffit.predict()
npt.assert_equal(pred.shape, data.shape)
# Should be possible to predict using a different gtab:
new_gtab = grad.gradient_table(bvals[::2], bvecs[::2])
new_pred = sffit.predict(new_gtab)
npt.assert_equal(
new_pred.shape,
data.shape[:-1] + bvals[::2].shape,
)
npt.assert_equal(new_pred[0, 0, 0], 0)
# Should be possible to predict for a single direction:
new_gtab = grad.gradient_table(bvals[1][None], bvecs[1][None, :])
new_pred = sffit.predict(new_gtab)
npt.assert_equal(new_pred.shape, data.shape[:-1])
npt.assert_equal(new_pred[0, 0, 0], 0)
def test_reconst_ivim():
with TemporaryDirectory() as out_dir:
bvals = np.array([
0., 10., 20., 30., 40., 60., 80., 100., 120., 140., 160., 180.,
200., 300., 400., 500., 600., 700., 800., 900., 1000.
])
N = len(bvals)
bvecs = generate_bvecs(N)
temp_bval_path = pjoin(out_dir, "temp.bval")
np.savetxt(temp_bval_path, bvals)
temp_bvec_path = pjoin(out_dir, "temp.bvec")
np.savetxt(temp_bvec_path, bvecs)
gtab = gradient_table(bvals, bvecs)
S0, f, D_star, D = 1000.0, 0.132, 0.00885, 0.000921
mevals = np.array(([D_star, D_star, D_star], [D, D, D]))
# This gives an isotropic signal.
data = multi_tensor(gtab,
mevals,
snr=None,
S0=S0,
fractions=[f * 100, 100 * (1 - f)])
# Single voxel data
data_single = data[0]
temp_affine = np.eye(4)
data_multi = np.zeros((2, 2, 1, len(gtab.bvals)))
data_multi[0, 0, 0] = data_multi[0, 1, 0] = data_multi[
1, 0, 0] = data_multi[1, 1, 0] = data_single
data_img = nib.Nifti1Image(data_multi.astype(int), temp_affine)
data_path = pjoin(out_dir, 'tmp_data.nii.gz')
nib.save(data_img, data_path)
mask = np.ones_like(data_multi[..., 0])
mask_img = nib.Nifti1Image(mask.astype(np.uint8), data_img.affine)
mask_path = pjoin(out_dir, 'tmp_mask.nii.gz')
nib.save(mask_img, mask_path)
ivim_flow = ReconstIvimFlow()
args = [data_path, temp_bval_path, temp_bvec_path, mask_path]
ivim_flow.run(*args, out_dir=out_dir)
S0_path = ivim_flow.last_generated_outputs['out_S0_predicted']
S0_data = nib.load(S0_path).get_data()
assert_equal(S0_data.shape, data_img.shape[:-1])
f_path = ivim_flow.last_generated_outputs['out_perfusion_fraction']
f_data = nib.load(f_path).get_data()
assert_equal(f_data.shape, data_img.shape[:-1])
D_star_path = ivim_flow.last_generated_outputs['out_D_star']
D_star_data = nib.load(D_star_path).get_data()
assert_equal(D_star_data.shape, data_img.shape[:-1])
D_path = ivim_flow.last_generated_outputs['out_D']
D_data = nib.load(D_path).get_data()
assert_equal(D_data.shape, data_img.shape[:-1])
def test_recursive_response_calibration():
"""
Test the recursive response calibration method.
"""
SNR = 100
S0 = 1
_, fbvals, fbvecs = get_fnames('small_64D')
bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
sphere = get_sphere('symmetric724')
gtab = gradient_table(bvals, bvecs)
evals = np.array([0.0015, 0.0003, 0.0003])
evecs = np.array([[0, 1, 0], [0, 0, 1], [1, 0, 0]]).T
mevals = np.array(([0.0015, 0.0003, 0.0003],
[0.0015, 0.0003, 0.0003]))
angles = [(0, 0), (90, 0)]
where_dwi = lazy_index(~gtab.b0s_mask)
S_cross, _ = multi_tensor(gtab, mevals, S0, angles=angles,
fractions=[50, 50], snr=SNR)
S_single = single_tensor(gtab, S0, evals, evecs, snr=SNR)
data = np.concatenate((np.tile(S_cross, (8, 1)),
np.tile(S_single, (2, 1))),
axis=0)
odf_gt_cross = multi_tensor_odf(sphere.vertices, mevals, angles, [50, 50])
odf_gt_single = single_tensor_odf(sphere.vertices, evals, evecs)
response = recursive_response(gtab, data, mask=None, sh_order=8,
peak_thr=0.01, init_fa=0.05,
init_trace=0.0021, iter=8, convergence=0.001,
parallel=False)
csd = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd.fit(data)
assert_equal(np.all(csd_fit.shm_coeff[:, 0] >= 0), True)
fodf = csd_fit.odf(sphere)
directions_gt_single, _, _ = peak_directions(odf_gt_single, sphere)
directions_gt_cross, _, _ = peak_directions(odf_gt_cross, sphere)
directions_single, _, _ = peak_directions(fodf[8, :], sphere)
directions_cross, _, _ = peak_directions(fodf[0, :], sphere)
ang_sim = angular_similarity(directions_cross, directions_gt_cross)
assert_equal(ang_sim > 1.9, True)
assert_equal(directions_cross.shape[0], 2)
assert_equal(directions_gt_cross.shape[0], 2)
ang_sim = angular_similarity(directions_single, directions_gt_single)
assert_equal(ang_sim > 0.9, True)
assert_equal(directions_single.shape[0], 1)
assert_equal(directions_gt_single.shape[0], 1)
sphere = Sphere(xyz=gtab.gradients[where_dwi])
sf = response.on_sphere(sphere)
S = np.concatenate(([response.S0], sf))
tenmodel = dti.TensorModel(gtab, min_signal=0.001)
tenfit = tenmodel.fit(S)
FA = fractional_anisotropy(tenfit.evals)
FA_gt = fractional_anisotropy(evals)
assert_almost_equal(FA, FA_gt, 1)
btable = np.loadtxt(get_data('dsi515btable'))
gtab = gradient_table(btable[:, 0], btable[:, 1:])
"""
Let's create a multi tensor with 2 fiber directions at 60 degrees.
"""
evals = np.array([[0.0015, 0.0003, 0.0003], [0.0015, 0.0003, 0.0003]])
directions = [(-30, 0), (30, 0)]
fractions = [50, 50]
signal, _ = multi_tensor(gtab,
evals,
100,
angles=directions,
fractions=fractions,
snr=None)
sphere = get_sphere('symmetric724').subdivide(1)
odf_gt = multi_tensor_odf(sphere.vertices,
evals,
angles=directions,
fractions=fractions)
"""
Perform the reconstructions with standard DSI and DSI with deconvolution.
"""
dsi_model = DiffusionSpectrumModel(gtab)